NADPH soak of Y316A mutant of corn root ferredoxin:NADP+ reductase

Experimental Data Snapshot

  • Resolution: 1.61 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.133 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


High-resolution studies of hydride transfer in the ferredoxin:NADP(+) reductase superfamily.

Kean, K.M.Carpenter, R.A.Pandini, V.Zanetti, G.Hall, A.R.Faber, R.Aliverti, A.Karplus, P.A.

(2017) FEBS J 284: 3302-3319

  • DOI: https://doi.org/10.1111/febs.14190
  • Primary Citation of Related Structures:  
    5VW2, 5VW3, 5VW4, 5VW5, 5VW6, 5VW7, 5VW8, 5VW9, 5VWA, 5VWB

  • PubMed Abstract: 

    Ferredoxin: NADP + reductase (FNR) is an FAD-containing enzyme best known for catalysing the transfer of electrons from ferredoxin (Fd) to NADP + to make NADPH during photosynthesis. It is also the prototype for a broad enzyme superfamily, including the NADPH oxidases (NOXs) that all catalyse similar FAD-enabled electron transfers between NAD(P)H and one-electron carriers. Here, we define further mechanistic details of the NAD(P)H ⇌ FAD hydride-transfer step of the reaction based on spectroscopic studies and high-resolution (~ 1.5 Å) crystallographic views of the nicotinamide-flavin interaction in crystals of corn root FNR Tyr316Ser and Tyr316Ala variants soaked with either nicotinamide, NADP + , or NADPH. The spectra obtained from FNR crystal complexes match those seen in solution and the complexes reveal active site packing interactions and patterns of covalent distortion of the FAD that imply significant active site compression that would favour catalysis. Furthermore, anisotropic B-factors show that the mobility of the C4 atom of the nicotinamide in the FNR:NADP + complex has a directionality matching that expected for boat-like excursions of the nicotinamide ring thought to enhance hydride transfer. Arguments are made for the relevance of this binding mode to catalysis, and specific consideration is given to how the results extrapolate to provide insight to structure-function relations for the membrane-bound NOX enzymes for which little structural information has been available. Structural data are available in the PDB database under the accession numbers 3LO8 (wild-type), 5VW4 [Y316S:nicotinamide (P3 2 21)], 5VW9 [Y316S:nicotinamide (P3 1 21)], 5VW3 [Y316S:NADP + (P3 2 21)], 5VW8 [Y316S:NADP + (P3 1 21)], 5VW2 [Y316S:NADPH (P3 2 21)], 5VW5 [Y316A:nicotinamide (P3 2 21)], 5VW6 [Y316A:NADP + (P3 2 21)], 5VW7 [Y316A:NADPH (P3 2 21)], 5VWA [Y316F (P3 2 21)], and 5VWB [Y316F:NADP + (P3 1 21)]. Enzyme Commission number: ferredoxin:NADP + reductase - E C1.18.1.2.

  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferredoxin--NADP reductase316Zea maysMutation(s): 1 
Find proteins for B4G043 (Zea mays)
Explore B4G043 
Go to UniProtKB:  B4G043
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4G043
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.61 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.133 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.188α = 90
b = 59.188β = 90
c = 188.032γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM119227
National Science Foundation (NSF, United States)United StatesMCB-9982727

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-23
    Type: Initial release
  • Version 1.1: 2017-10-11
    Changes: Database references
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description